SBC logo Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred

Fetching Q6ZUB1 from www.uniprot.org...

The NucPred score for your sequence is 0.88 (see score help below)

   1  MGNLVIPLGKGRAGRVESGQRIPPPAPRPSVECTGDDIALQMEKMLFPLK    50
  51  SPSATWLSPSSTPWMMDFILTSVCGLVLLFLLLLYVHSDPPSPPPGRKRS   100
 101  SREPQRERSGRSRSRKISALKACRILLRELEETRDLNYLLESHLRKLAGE   150
 151  GSSHLPLGGDPLGDVCKPVPAKAHQPHGKCMQDPSPASLSPPAPPAPLAS   200
 201  TLSPGPMTFSEPFGPHSTLSASGPPEPLLPLKCPATQPHVVFPPSPQPHG   250
 251  PLASSPPPPDSSLAGLQCGSTTCPVPQSSPLHNQVLPPPTRVISGLGCSS   300
 301  DPIWDLYCWREAATTWGLSTYSHGKSQPRHLPDHTSEASFWGDPTPKHME   350
 351  VGGCTFIHPDVQKLLETLIAKRALMKMWQEKERKRADHPHMTSLGKEWDI   400
 401  TTLNPFWNVSTQPQQLPRPQQVSDATTVGNHLQQKRSQLFWDLPSLNSES   450
 451  LATTVWVSRNPSSQNAHSVPLDKASTSLPGEPEVEASSQLSQAPPQPHHM   500
 501  AQPQHFTPAWPQSQPPPLAEIQTQAHLSPPVPSLGCSSPPQIRGCGASYP   550
 551  TSQERTQSVIPTGKEYLEWPLKKRPKWKRVLPSLLKKSQAVLSQPTAHLP   600
 601  QERPASWSPKSAPILPGVVTSPELPEHWWQGRNAIHQEQSCGPPSRLQAS   650
 651  GDLLQPDGEFPGRPQSQAEDTQQALLPSQPSDFAGKGRKDVQKTGFRSSG   700
 701  RFSDKGCLGSKLGPDPSRDQGSGRTSVKALDEDKEAEGDLRRSWKYQSVS   750
 751  STPRDPDKEHLENKLQIHLARKVGEIKEGWIPMPVRRSWLMAKCAVPKSD   800
 801  THRKPGKLASWRGGKAHVNTSQELSFLHPCTQQILEVHLVRFCVRHSWGT   850
 851  DLQSLEPINVWSGEAQAPPFPQSTFTPWASWVSRVESVPKVPIFLGKRPQ   900
 901  NGPGDNRTTSKSVPTVSGPLAAPPPEQEGVQRPPRGSQSADTHGRSEAFP   950
 951  TGHKGRGCSQPPTCSLVGRTWQSRTVLESGKPKPRLEGSMGSEMAGNEAW  1000
1001  LESESMSPGDPCSSRALQVLSIGSQWARAEDALQALKVGEKPPTWEVTLG  1050
1051  ASVRASSGSVQEDLRSTGALGTTGNPSASSVCVAQDPEQLHLKAQVVSEI  1100
1101  ALIVQVDSEEQLPGRAPGILLQDGATGLCLPGRHMDMLTAADRLPTQAPL  1150
1151  STSQSVSGKNMTASQGPCALLWKGGDSPGQQEPGSPKAKAPQKSQKTLGC  1200
1201  ADKGEAHRRPRTGEQGHRSKGPRTSEASGRSHPAQAREIGDKQERKYNQL  1250
1251  QLEKGQTPPESHFQRKISHHPQGLHPRKGGTRWEDVLQKGKPGADAFQSW  1300
1301  GSGPPRQFMDCMADKAWTISRVVGQILVDKLGLQWGRGPSEVNRHKGDFR  1350
1351  AQENVPSCCHRGHCHQERSREMRALACSPKATPKGHHCPVKNRGIRDRDS  1400
1401  SWAPPPREPVSPAGPHHHRPRMASTSGGPHPQLQELMSAQRCLAS       1445

Positively and negatively influencing subsequences are coloured according to the following scale:

(non-nuclear) negative ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| positive (nuclear)

with NucPred



If you find NucPred useful, please cite this paper:
NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022
The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold Specificity Sensitivity
see above fraction of proteins predicted to be nuclear that actually are nuclear fraction of true nuclear proteins that are predicted (coverage)
0.10 0.45 0.88
0.20 0.52 0.83
0.30 0.57 0.77
0.40 0.63 0.69
0.50 0.70 0.62
0.60 0.71 0.53
0.70 0.81 0.44
0.80 0.84 0.32
0.90 0.88 0.21
1.00 1.00 0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

Go back to the NucPred Home Page.